Current oncology drug development is designed to target specific cellular signaling pathways critical for tumor growth and progression so that therapies are more specific compared to traditional chemotherapy. Signaling pathway specific biomarkers and gene expression signatures facilitate such targeted drug development activities. The Wnt/β-catenin pathway is one of the most frequently perturbed pathways in human cancers and an important target for oncology drug development. This study identified a set of genes that provide a gene signature for evaluating the Wnt/β-catenin pathway and developed a companion scoring algorithm to convert gene expression data into a score that serves as an indicator for Wnt/β-catenin signaling pathway activity. High density microarray gene expression profiling was carried out on 293H cells treated with Wnt3a protein and β-catenin specific siRNA. Sixty four (64) genes were selected on the basis of statistically significant upregulation of expression in response to Wnt3a and reversion of upregulated expression by treatment with β-catenin siRNA. These 64 Wnt/β-catenin response genes were further evaluated by real-time PCR on 21 samples from a panel of 16 different cell lines either stimulated with Wnt3a and LiCl or inhibited with β-catenin siRNA. Using a support vector machine classifier method, 16 genes out of the 64 were identified as a gene expression signature for the Wnt/β-catenin signaling pathway. The sensitivity of identified gene expression signature was assessed using LNCaP and SW480 cells treated with pyrvinium, a Wnt/β-catenin pathway inhibitor. The gene expression signature successfully identified successive decreases in Wnt/β-catenin signaling pathway activity by pyrvinium treatment, in a dose dependent manner. Importantly, detection of decreased Wnt/β-catenin signaling activity by gene expression signature preceded the detection of down-regulation of active β-catenin protein levels by western blot. A similar result was observed in HCT116 cells treated with another Wnt/β-catenin pathway inhibitor, CCT036477. On the other hand, although gene expression signature was able to report a dose dependent upregulation of Wnt/β-catenin pathway activity in 293H cells treated with CHIR99021, a known Wnt pathway stimulator and a specific inhibitor of GSK3β activity, the signature failed to respond in a dose dependent manner in HT1080 and MDA-MB-231 cells with CHIR99021 treatment. Taken together, this study demonstrates the feasibility of developing a gene expression signature that can serve as a pharmacodynamic biomarker to monitor the regulatory status of cellular Wnt/β-catenin pathway activity.

The gene panels and algorithms presented here are intended for molecular biology applications. The panels and/or algorithms are not intended for diagnosis, prevention or treatment of a disease.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A43.